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- PDB-5ja5: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -

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Basic information

Entry
Database: PDB / ID: 5ja5
TitleCrystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A and L130A mutant in complex with rice D53 repressor EAR peptide motif
Components
  • Protein TPR1
  • The rice D53 peptide (a.a. 794-808)
KeywordsTRANSCRIPTION / TRANSCRIPTION REPRESSION / TRANSCRIPTIONAL COREPRESSOR TOPLESS / ALPHA-HELICAL STRUCTURE / TETRAMER / TRANSCRIPTIONAL REPRESSOR D53
Function / homology
Function and homology information


positive regulation of pattern recognition receptor signaling pathway / response to strigolactone / protein sequestering activity / regulation of DNA-templated transcription / nucleus / plasma membrane
Similarity search - Function
: / TOPLESS, zinc finger domain / Topless family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Clp repeat (R) domain profile. ...: / TOPLESS, zinc finger domain / Topless family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein DWARF 53 / Protein TPR1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKe, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
Citation
Journal: Sci Adv / Year: 2017
Title: A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex.
Authors: Ma, H. / Duan, J. / Ke, J. / He, Y. / Gu, X. / Xu, T.H. / Yu, H. / Wang, Y. / Brunzelle, J.S. / Jiang, Y. / Rothbart, S.B. / Xu, H.E. / Li, J. / Melcher, K.
#1: Journal: Sci Adv / Year: 2015
Title: Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors.
Authors: Ke, J. / Ma, H. / Gu, X. / Thelen, A. / Brunzelle, J.S. / Li, J. / Xu, H.E. / Melcher, K.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TPR1
B: The rice D53 peptide (a.a. 794-808)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7503
Polymers26,6842
Non-polymers651
Water2,810156
1
A: Protein TPR1
B: The rice D53 peptide (a.a. 794-808)
hetero molecules

A: Protein TPR1
B: The rice D53 peptide (a.a. 794-808)
hetero molecules

A: Protein TPR1
B: The rice D53 peptide (a.a. 794-808)
hetero molecules

A: Protein TPR1
B: The rice D53 peptide (a.a. 794-808)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,99912
Polymers106,7388
Non-polymers2624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)57.317, 57.317, 173.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Protein TPR1 / Aberrant spikelet and panicle1-related 2 / Protein ASP1-RELATED 2 / OsASPR2 / Topless-related ...Aberrant spikelet and panicle1-related 2 / Protein ASP1-RELATED 2 / OsASPR2 / Topless-related protein 1 / Topless-related protein 2 / OsTPR2


Mass: 24819.451 Da / Num. of mol.: 1 / Fragment: N-terminal topless domain (UNP residues 1-209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice)
Gene: TPR1, ASPR2, TPR2, Os01g0254100, LOC_Os01g15020, OsJ_01134, OSNPB_010254100, P0705D01.10-1
Production host: Escherichia coli (E. coli) / References: UniProt: Q5NBT9
#2: Protein/peptide The rice D53 peptide (a.a. 794-808)


Mass: 1864.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice) / References: UniProt: Q2RBP2*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20% w/v Polyethylene glycol 3350, 0.2 M Potassium phosphate monobasic, pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2015
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20502 / % possible obs: 100 % / Redundancy: 15.6 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 16 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHE

4zhe


Resolution: 2→29.612 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 23.79
RfactorNum. reflection% reflection
Rfree0.2278 1869 5.01 %
Rwork0.2031 --
obs0.2043 20429 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 1 156 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051764
X-RAY DIFFRACTIONf_angle_d0.8472368
X-RAY DIFFRACTIONf_dihedral_angle_d14.856664
X-RAY DIFFRACTIONf_chiral_restr0.035262
X-RAY DIFFRACTIONf_plane_restr0.003299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05410.32281560.26822712X-RAY DIFFRACTION100
2.0541-2.11460.34931530.24132720X-RAY DIFFRACTION100
2.1146-2.18280.25211240.22162734X-RAY DIFFRACTION100
2.1828-2.26080.341110.2672747X-RAY DIFFRACTION100
2.2608-2.35130.21051550.20732692X-RAY DIFFRACTION100
2.3513-2.45820.29061550.20212761X-RAY DIFFRACTION100
2.4582-2.58780.21251440.20322713X-RAY DIFFRACTION100
2.5878-2.74980.2491660.20912698X-RAY DIFFRACTION100
2.7498-2.96190.26261430.20612719X-RAY DIFFRACTION100
2.9619-3.25970.22991220.20822748X-RAY DIFFRACTION100
3.2597-3.73050.19061370.20742728X-RAY DIFFRACTION100
3.7305-4.69710.20211450.16732740X-RAY DIFFRACTION100
4.6971-29.61540.20021580.19872708X-RAY DIFFRACTION100

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